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Fulltext Swiftlets and edible bird’s nest industry in Asia

Looi, Qi Hao, Abdul Rahman Omar

The Pertanika Journal of Scholarly Research Reviews, 2016;2(1):32-48.
MyJurnal

Swiftlet
s
are small insectivorous birds which breed throughout Southeast Asia and
the South Pacific.
Among many swiftle
t species, only a few are notable to produce edible bird’s
nest
s
(EBN) from the secreted saliva during breeding seasons.
The taxonomy of swiftlet
s
remains one of the most controversial in the avian species due to the high similarity in
morphological charac
teristics among the species. Over the last few decades, researchers have
studied the taxonomy of swiftlet
s
based on the morphological
trade
, behavior, and genetic
traits
.
However, despite all the efforts,
the
swiftlet taxonomy remains unsolved.
The
EBN is one of
the
most expensive animal products
and frequently being referred
to
as the “
Caviar of the East
”.
The
EBN market value varies from
US
$1000.00 to
US
$10,000.00 per kilogram depend
ing
on
its grade, shape, type and origin.
Hence, bird’s nest harve
sting is considered a lucrative industry
in many countries in Southeast Asia.
However,
the
industry faced several challenges over the
decades such as the authenticity of the EBN, the quality assurance and the depletion of swiftlet
population. Furthermore,
there is limited scientific evidence regarding EBN’s medical benefits
as
claimed by manufacturers. This paper reviews the taxonomy of swiftlet
s
, its morphological
characteristics, the challenges currently encountered by the industry, and finally the
compos
ition and medical benefits of EBN.
Fulltext Development of an Automated Biaxial Solar Photovoltaic Tracking System

Ahmad Maliki Omar, Muhamad Rizuan Yahir, Sulaiman Shaari, Abdul Rahman Omar

Scientific Research Journal, 2006;3(2):3-12.
MyJurnal

This paper presents and describes a prototype product code-named SolT2A
which is a system that tracks the position of the sun automatically across the
celestial vault in two axes. This kind of system is typically used in a solar
photovoltaic (PV) system in terrestrial applications to provide electrical
power. It is designed and fabricated due to Malaysia’s location near the
equator, thus the solar altitude crosses the zenith and the azimuth reverses
direction during the year. Thus the use of a static PV system is not maximised
during half of the year. This situation can be addressed by using a two-axes
solar tracking system. So far, Malaysia has not implemented such powertracking
systems. Thus SolT2A has been designed and fabricated to address
the problem by using a combination of electro-mechanical devices with an
element of programming ingenuity and intelligence. Basically SolT2A
measures solar irradiance at four points and makes comparisons in terms of
the intensity received. These data are then analysed and processed by a
controller before being sent to a DC motor that ensures the maximum amount
of solar irradiance received on the PV panels all the time. Thus SolT2A is a
system that maximises the power output of the PV panels to obtain the highest
Fulltext Determining the efficacy of CRISPR-Cas9 mechanisms on the uppP Gene of Klebsiella pneumonia using Lysozyme assay

Mohd Nasharudin Razak, Raha Abdul Rahim, Abdul Rahman Omar, Zunita Zakaria, Nurulfiza Mat Isa

Malaysian Journal of Medicine and Health Sciences, 2020;16(4):226-233.
MyJurnal

Introduction: Multidrug resistance bacteria is alarming worldwide. A lot of research were done and are ongoing to search for the best, convenient and economically affordable ways to fight them. With the latest genome editing tool; Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology, this research was performed to develop a novel strategy to genetically modify the genome and inhibit the growth of Klebsiella pneumoniae (UPM ESBLKP1), an Extended Spectrum Beta Lactamases (ESBL) organism. Methods: A CRISPR-Cas9 vector was construct- ed together with guide RNAs designed specifically for the targeted uppP gene, a gene responsible for bacterial cell growth and protection. Results: The growth and cell wall integrity of the modified Klebsiella pneumoniae (UPM ESBLKP1) were significantly inhibited and reduced, respectively. Interestingly, wild type Klebsiella pneumoniae showed a normal growth curve while modified strains showed a faster doubling rate when supplemented with Luria-Bertani media. In contrast, slower growth rate of modified strain was observed in the M9 minimal media. This explained the higher doubling rate of mutants on nutrient rich medium earlier is being related to gene recovery. They grew slowly in the minimal media as they were adapting to a new environment while recovering the uppP gene and surviving, proving the success of its gene modification. Conclusion: The developed CRISPR-gRNA system was able to modify the targeted Klebsiella pneumoniae gene hence providing an opportunity to develop a new drug for Klebsiella pneumoniae infection as an alternative to antibiotics.
Fulltext Discrimination of Escherichia coli isolates recovered from mucosal contents of chicken intestines and different age by repetitive elements sequence-based PCR

Mohd Asrore Mohd Shaufi, Chin, Chin Sieo, Abdul Rahman Omar, Yin, Wan Ho, Cheah, Yoke-Kqueen, Chun, Wie Chong, et al.

Journal of Biochemistry, Microbiology and Biotechnology, 2017;5(1):7-12.
MyJurnal

Repetitive sequence-based PCR (rep-PCR) is a distinctive typing approach that is used to
differentiate between bacterial strains. This method is also useful for studying bacterial diversity
from different sources. In this study, four rep-PCR which are enterobacterial repetitive intergenic
consensus PCR (ERIC-PCR), BOX-PCR, repetitive extragenic palindromic PCR (REP-PCR)
and polytrinucleotide (GTG)5-PCR were evaluated for differentiation of eighteen Escherichia
coli isolates to correct source based on part of intestine and age. These isolates were recovered
earlier from ileal and caecal mucosal contents of chickens at different age. The purpose of this
study was to investigate the efficacy of four rep-PCR methods and composite of rep-PCR
patterns to differentiate E. coli isolates to original sources of part of intestines and age based on
the D index (discriminatory power determined based on Simpson’s index of diversity calculated
at similarity coefficient of 90%). The (GTG)5-PCR had the highest D index (0.9804) for part of
intestine and age factors. The similar D index was observed in the composite of rep-PCR
patterns. The lowest D index was observed in ERIC- and BOX-PCR at 0.9020 and 0.8039 for
part of intestine and age factors, respectively. (GTG)5-PCR was also the most discriminative rep-
PCR observed due to its ability to cluster 14I 3E and 14I 2X isolates, and 14C 1E and 14C 3E
isolates correctly in part of intestine and age factors. It was concluded that (GTG)5-PCR is a
promising tool for discriminating E. coli isolates extracted from chicken intestines.
Production of phytase by mitsuokella jalaludinii in semi-solid state fermentation of agricultural by-products

Tang HC, Sieo CC, Abdul Rahman Omar, Ho YW, Norhani Abdullah, Rosfarizan Mohamad, et al.

Sains Malaysiana, 2018;47:277-286.

Phytase activity and growth of anaerobic rumen bacterium, Mitsuokella jalaludinii were investigated by semi-solid
state fermentation. Carbon source (rice bran, yam and cassava), nitrogen sources (soya bean, offal meal, fish meal and
feather meal) and growth factors (hemin, L-cysteine hydrochloride and minerals) were evaluated in a one-factor-at-atime
approach. Rice bran and fish meal produced better growth and phytase enzyme activity. The removal of L-cysteine
hydrochloride and minerals significantly decreased (p<0.05) phytase activity from 1178.72 U to 446.99 U and 902.54
U, respectively. The response surface methods (RSM) was conducted to optimize the phytase production and the results
showed the combination of 7.7% of rice bran and 3.7% of fish meal in semi-solid state fermentation gave the highest
phytase activity. Maximum phytase production and optimum growth of bacteria were detected at 12 h incubation in both
MF medium (control) and agro-medium. In this agro-medium, M. jalaludinii produced 2.5 fold higher phytase activity
compared to MF medium.
Fulltext Isolation and molecular characterization of type I and type II feline coronavirus in Malaysia

Amer A, Siti Suri A, Abdul Rahman O, Mohd HB, Faruku B, Saeed S, et al.

Virol J, 2012 Nov 21;9:278.
PMID: 23171743 DOI: 10.1186/1743-422X-9-278

BACKGROUND: Feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV) are two important coronaviruses of domestic cat worldwide. Although FCoV is prevalent among cats; the fastidious nature of type I FCoV to grow on cell culture has limited further studies on tissue tropism and pathogenesis of FCoV. While several studies reported serological evidence for FCoV in Malaysia, neither the circulating FCoV isolated nor its biotypes determined. This study for the first time, describes the isolation and biotypes determination of type I and type II FCoV from naturally infected cats in Malaysia.
FINDINGS: Of the total number of cats sampled, 95% (40/42) were RT-PCR positive for FCoV. Inoculation of clinical samples into Crandell feline kidney cells (CrFK), and Feline catus whole fetus-4 cells (Fcwf-4), show cytopathic effect (CPE) characterized by syncytial cells formation and later cell detachment. Differentiation of FCoV biotypes using RT-PCR assay revealed that, 97.5% and 2.5% of local isolates were type I and type II FCoV, respectively. These isolates had high sequence homology and phylogenetic similarity with several FCoV isolates from Europe, South East Asia and USA.
CONCLUSIONS: This study reported the successful isolation of local type I and type II FCoV evident with formation of cytopathic effects in two types of cell cultures namely the CrFK and Fcwf-4 , where the later cells being more permissive. However, the RT-PCR assay is more sensitive in detecting the antigen in suspected samples as compared to virus isolation in cell culture. The present study indicated that type I FCoV is more prevalent among cats in Malaysia.
Rubinstein-Taybi syndrome in diverse populations

Tekendo-Ngongang C, Owosela B, Fleischer N, Addissie YA, Malonga B, Badoe E, et al.

Am J Med Genet A, 2020 12;182(12):2939-2950.
PMID: 32985117 DOI: 10.1002/ajmg.a.61888

Rubinstein-Taybi syndrome (RSTS) is an autosomal dominant disorder, caused by loss-of-function variants in CREBBP or EP300. Affected individuals present with distinctive craniofacial features, broad thumbs and/or halluces, and intellectual disability. RSTS phenotype has been well characterized in individuals of European descent but not in other populations. In this study, individuals from diverse populations with RSTS were assessed by clinical examination and facial analysis technology. Clinical data of 38 individuals from 14 different countries were analyzed. The median age was 7 years (age range: 7 months to 47 years), and 63% were females. The most common phenotypic features in all population groups included broad thumbs and/or halluces in 97%, convex nasal ridge in 94%, and arched eyebrows in 92%. Face images of 87 individuals with RSTS (age range: 2 months to 47 years) were collected for evaluation using facial analysis technology. We compared images from 82 individuals with RSTS against 82 age- and sex-matched controls and obtained an area under the receiver operating characteristic curve (AUC) of 0.99 (p
Cover Image, Volume 173A, Number 4, April 2017

Kruszka P, Addissie YA, McGinn DE, Porras AR, Biggs E, Share M, et al.

Am J Med Genet A, 2017 Apr;173(4):i.
PMID: 28328119 DOI: 10.1002/ajmg.a.38224

The cover image, by Paul Kruszka et al., is based on the Original Article 22q11.2 deletion syndrome in diverse populations, DOI: 10.1002/ajmg.a.38199. Individual images are property of the National Human Genome Research Institute and are in the public domain.
Fulltext 22q11.2 deletion syndrome in diverse populations

Kruszka P, Addissie YA, McGinn DE, Porras AR, Biggs E, Share M, et al.

Am J Med Genet A, 2017 Apr;173(4):879-888.
PMID: 28328118 DOI: 10.1002/ajmg.a.38199

22q11.2 deletion syndrome (22q11.2 DS) is the most common microdeletion syndrome and is underdiagnosed in diverse populations. This syndrome has a variable phenotype and affects multiple systems, making early recognition imperative. In this study, individuals from diverse populations with 22q11.2 DS were evaluated clinically and by facial analysis technology. Clinical information from 106 individuals and images from 101 were collected from individuals with 22q11.2 DS from 11 countries; average age was 11.7 and 47% were male. Individuals were grouped into categories of African descent (African), Asian, and Latin American. We found that the phenotype of 22q11.2 DS varied across population groups. Only two findings, congenital heart disease and learning problems, were found in greater than 50% of participants. When comparing the clinical features of 22q11.2 DS in each population, the proportion of individuals within each clinical category was statistically different except for learning problems and ear anomalies (P
Down syndrome in diverse populations

Kruszka P, Porras AR, Sobering AK, Ikolo FA, La Qua S, Shotelersuk V, et al.

Am J Med Genet A, 2017 Jan;173(1):42-53.
PMID: 27991738 DOI: 10.1002/ajmg.a.38043

Down syndrome is the most common cause of cognitive impairment and presents clinically with universally recognizable signs and symptoms. In this study, we focus on exam findings and digital facial analysis technology in individuals with Down syndrome in diverse populations. Photos and clinical information were collected on 65 individuals from 13 countries, 56.9% were male and the average age was 6.6 years (range 1 month to 26 years; SD = 6.6 years). Subjective findings showed that clinical features were different across ethnicities (Africans, Asians, and Latin Americans), including brachycephaly, ear anomalies, clinodactyly, sandal gap, and abundant neck skin, which were all significantly less frequent in Africans (P
Fulltext Noonan syndrome in diverse populations

Kruszka P, Porras AR, Addissie YA, Moresco A, Medrano S, Mok GTK, et al.

Am J Med Genet A, 2017 Sep;173(9):2323-2334.
PMID: 28748642 DOI: 10.1002/ajmg.a.38362

Noonan syndrome (NS) is a common genetic syndrome associated with gain of function variants in genes in the Ras/MAPK pathway. The phenotype of NS has been well characterized in populations of European descent with less attention given to other groups. In this study, individuals from diverse populations with NS were evaluated clinically and by facial analysis technology. Clinical data and images from 125 individuals with NS were obtained from 20 countries with an average age of 8 years and female composition of 46%. Individuals were grouped into categories of African descent (African), Asian, Latin American, and additional/other. Across these different population groups, NS was phenotypically similar with only 2 of 21 clinical elements showing a statistically significant difference. The most common clinical characteristics found in all population groups included widely spaced eyes and low-set ears in 80% or greater of participants, short stature in more than 70%, and pulmonary stenosis in roughly half of study individuals. Using facial analysis technology, we compared 161 Caucasian, African, Asian, and Latin American individuals with NS with 161 gender and age matched controls and found that sensitivity was equal to or greater than 94% for all groups, and specificity was equal to or greater than 90%. In summary, we present consistent clinical findings from global populations with NS and additionally demonstrate how facial analysis technology can support clinicians in making accurate NS diagnoses. This work will assist in earlier detection and in increasing recognition of NS throughout the world.
Cover Image, Volume 173A, Number 9, September 2017

Kruszka P, Porras AR, Addissie YA, Moresco A, Medrano S, Mok GTK, et al.

Am J Med Genet A, 2017 Sep;173(9):i.
PMID: 28816424 DOI: 10.1002/ajmg.a.38408

The cover image, by Paul Kruszka et al., is based on the Original Article Noonan Syndrome in Diverse Populations, DOI: 10.1002/ajmg.a.38362. Design Credit: Darryl Leja.
Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms

Kaur M, Blair J, Devkota B, Fortunato S, Clark D, Lawrence A, et al.

Am J Med Genet A, 2023 Aug;191(8):2113-2131.
PMID: 37377026 DOI: 10.1002/ajmg.a.63247

Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (>60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS-like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or "DTRs"). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype-phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population.

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